Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Abstract

Summary Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor‐bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R‐genes harbour more SNPs than variable genes. More nucleotide binding site‐leucine‐rich repeat (NBS‐LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics‐based improvement and improved disease resistance.

SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation

“…Genome-wide structural variations are hypothesized to drive important phenotypic variation within a species, and a number of CNVs and PAVs in R-genes across the species have been extensively documented [36][37][38][39] . In this study, the multi-species comparative analysis showed that a large number of candidate genes affected by CNVs associate with various abiotic and biotic stresses, flower development, flowering time and reproduction.…”

Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era

“…Valuable genomics resources for interrogating the molecular aspects of Brassica –pathogen interactions have been provided via high-quality genome assemblies of Brassica species using PacBio sequencing, for example, B. rapa cultivar “Chiifu-401-42” [ 39 ], B. oleracea cultivar “C-8” [ 40 ], B. napus German winter cultivar “Express 617” [ 33 ] and the recent improved B. napus “Darmor- bzh ” [ 41 ], along with the highly contiguous B. nigra assembly, both achieved via ONT technology ( Table 1 ). These high-quality Brassica assemblies resolve the “difficult” genomic regions commonly found in polyploid crops [ 42 ], particularly highly repetitive DNA sequences related to transposable elements (TEs), copy number variation (CNV), presence–absence variation (PAV) and homoeologous exchange, many of which are associated with disease resistance genes [ 43 , 44 , 45 ].…”

“…Examples of RGAs include nucleotide-binding site leucine-rich repeats (NLRs), mainly comprising the TIR-NBS-LRR (TNL) and CC-NBS-LRR (CNL) types, receptor-like protein kinases (RLKs), receptor-like proteins (RLPs) and wall-associated kinases [ 53 , 54 ]. Using pangenomics, 106 RGAs have been identified within the Blackleg QTL in the B. napus pangenome [ 45 ] while 59 RGAs were detected within the Sclerotinia, Fusarium wilt and Clubroot resistance QTLs in the B. oleracea pangenome [ 43 ]. These pangenomics studies revealed that different classes of RGAs (RLKs, TNLs and others) show different percentages of variability across the lines, which leads to the following question: is there any association between R gene variability and resistance outcomes in Brassica crops for the major diseases?…”

The Use of Genetic and Gene Technologies in Shaping Modern Rapeseed Cultivars (Brassica napus L.)

“…In the pan-genome of B. oleracea , Bayer et al [ 67 ] found that the most abundant resistance gene analog (RGA) candidates in the additional pan-genome contigs were leucine rich repeat (NBS-LRR) genes compared to receptor-like kinase (RLK) and receptor-like protein (RLP) genes, and identified 59 RGA candidates linked to known QTL of Sclerotinia , clubroot, and Fusarium resistance. It was found that 753 out of the total 1749 RGAs in the pan-genome of B. napus [ 68 ] are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh), suggesting many genes relating to plant resistance mechanisms may be unknown.…”